Dawn of the Metroid
by Samsapoping
Summary: Upon returning to Lumiose City for his gym battle against Clemont, Ash and Co. discover a mysterious egg. After the gang get saved by Samus Aran from an invasion of Space Pirates, the egg hatches into a Metroid, who thinks that Bonnie is its mother. The universe is in the care of a little blonde girl. After Super Metroid: Slight Amourshipping
1. Chapter 1: Wishing Ships

**For those who were with me during the previous version of "Dawn of the Metroid", I'm sorry for recently deleting that story. I wasn't interested in continuing the story and from what it was going, it was going to cater towards the Pokemon fans. Basically, after Samus was going to tell her backstory to Ash, Dawn, and Brock, they were going to go to Kanto to give Prof. Oak the Metroid and I was going to have Misty be in it just to be jealous at Dawn and Ash being parents to the Metroid.**

**I think this version will be much more interesting and it's not going to be heavy on the shipping department.**

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**Enjoy!**

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Unknown POV

"I thought the galaxy was at peace."

"It wasn't!"

After I vanquished Mother Brain, Planet Zebes was no longer infested by Metroids. The galaxy was peaceful and I took some time off. Unfortunately, my break ended short by the Galactic Federation's call.

Recently, I received a new mission. I had to investigate Space Pirate activity on a peaceful planet and any signs of Metroids. A planet that was inhabited by humans and monsters was what I was told. With that much knowledge of what kind of world was in peril, I accepted the mission and flew off in my spaceship.

Upon entering the planet's orbit, I noticed a familiar creature flying towards my destination too. A silver mechanical dragon who had yellow wings that were made out of pure energy. A mechanical dragon who I thought was defeated for good by my own arm cannon. I had to stop this monster from destroying this new world. This beast may have destroyed my home planet K-12, but I'm not going to let him destroy another world

The planet itself looked beautiful with water covering most of its mass and huge lands divided into many different regions. With no time, I flew faster into my destination, chasing the winged machine towards the western side of the planet.

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**Meanwhile in the Kalos Region**

Normal POV

It was a dark and peaceful night outside near Lumiose City as our heroes decide to camp out by a lake. Rather than relaxing in the lit up, noisy city, the gang decided to enjoy the night down by the calming, peaceful body of water. Stars shimmering down at the reflecting liquid as a little blonde girl saw herself in her normal clothes.

"You okay, Bonnie?" A boy called.

The girl who saw her reflection was the Lumiose City's little sister. Part of her golden hair was tied up by a hairclip, forming a long ponytail that was sticking out from the left side of her head. A dark brown blouse with a black ribbon covered her chest. Lastly, her bottom had on a white skirt, black shorts to cover the upper part of her legs, and a pair of pink Mary Jane flats.

"Huh?" Bonnie turned around.

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Bonnie's POV

Standing behind me were the two trainers in charged of my care. The one who was the furthest away (and setting up her tent) was a beginner trainer who felt more like a big sister to me. A novice Pokemon Performer named Serena who was dressed up in her pink pajamas and wore a pink bow over her short, honey colored hair.

"You've been awfully quiet for a while." Serena exclaimed.

But the trainer who was concerned towards my silence was the raven haired boy from the Kanto region. He was the reason why we've been traveled together and why my older brother, Clemont wasn't with us during the last few weeks. Ever since we returned to Lumiose City after Ash won his fourth gym badge, my brother decided to stay at the gym for awhile, leaving me with Ash and Serena to go train with them. To help Serena become a better Pokemon Trainer, but more importantly, to see if Ash was worthy of winning the Volt Badge from my brother.

Instead of wearing his normal outfit, the future Pokemon Master wore a black, short sleeved shirt, a pair of blue jeans, and white socks. Along with him, was his adorable little electric mouse pokemon coming towards me. A yellow rodent with red cheeks, pointy ears with the tips of them being black, and a tail that was in the shape of a lightning bolt.

"Pi-ka-chu?" The mouse squeaked.

"I was?..." I blinked.

"Sorry. I was just wondering about something." I told my friends.

"You're thinking about Clemont, aren't you?" Ash guessed.

The trainer was partly right about my thoughts. I was wondering about my big brother, but there was another thought that made me even more curious than him. After travelling 2/3s of my home region and seeing so many exotic pokemon, I began to wonder what other types of pokemon wandered beyond us. I knew there were over six hundred pokemon inhabiting our tiny world, but were there other pokemon "out there".

"Well yeah, but there's something else interesting me?" I answered.

"What do you mean, Bonnie?" Serena asked me curiously.

"I'm talking about the universe." I clarified.

"The universe?" The trainers repeated.

The subject sounded odd to hear towards the two trainers. An eight year old girl wondering about the universe? Usually, a kid like me would wonder his/her future will be when they start their life as a Pokemon Trainer or the dreams they want to fulfill. But to me during this peaceful night, I was questioning about the universe, mainly pokemon wandering the cosmos.

"We all know that there are over six hundred pokemon in our world." I said, turning back up at the starry sky.

"Yes?" Serena responded.

"And Arceus created us, our world, pokemon, and the universe." I replied.

"Yeah,…and you're wondering?..." Ash questioned.

"What if there are other pokemon wandering throughout space?" I concluded.

It took a moment for Ash and Serena to understand what I was saying. Overwhelmed by my own question, I decided to repeat the question in simpler terms.

"Other pokemon that we've never seen before." I clarified.

Knowing that my friends were going to be lost in the thoughts, I allowed their silence to last for a bit. I wasn't the kind of girl who was intrigued in science, but the night sky had me wondering about the possibility of life. It was just a random thought that came to me and I thought it would be interesting to share it with my friends.

"What makes you think about that, Bonnie?" The Pokemon Performer asked me.

"I don't know." I answered, turning my head back up towards the sky.

"I was just gazing up at the stars and the thought just came to me." I replied.

"Well, I think it's an interesting question." Ash commented.

"Pika?" Pikachu spoke.

"Pokemon roaming in space besides Arceus, Dialga, Palkia, Rayquaza, and Deoxys?" The future Pokemon Master exclaimed.

"That would be awesome seeing one of those." He responded his own question.

As great minds thought alike, I turned my attention towards Ash who was sitting beside me. Despite it being a silly question, I watched the raven haired boy become fascinated by it. With his chocolate pupils gazing up at the sky, it seemed that he was also intrigued towards Astronomy or just pokemon discoveries in general. Whenever my brother would send out one of his unnecessary inventions, Ash would adore it until it explode in our faces. It made me question if he would rather be a Pokemon Scientist than a trainer.

"Pika!"

Suddenly, we were woken up by the sudden squeaks of Ash's Pikachu.

"What is it, Pikachu?" Ash turned to his partner.

"Look! A shooting star!" Serena cried.

In an instant, we all shot our heads back up and spotted what the performer pointed. Soaring across the darkness wasn't just a shooting star, but there was another one following its leader.

"There's two!" I noted excitedly.

Overwhelmed by the sudden excitement, I closed my eyes and folded my hands together. Like with normal stars, people have said that wishes from shooting stars were possible to be granted if I was hopeful for them. Now was the perfect time to see I was strong enough to see my dream come true.

**"I wish to see pokemon from other worlds!"**

With the wish made out, I unfolded myself and turned back towards my friends. It became no surprised finding them in the same position as I was as they were wishing on those stars too. From deep inside, I figured that Ash's wish was going to be related to pokemon as well. Whether it was for him winning the Kalos League or something similar to my wish, I predicted it to be a good one. As for Serena, I only had two guesses for her. Either she was wishing to become Kalos Queen or marry Ash.

Judging by the blushing face from my left, it was clear what the brunette wanted. After hearing the story of how the two first met back when they were kids at Prof. Oak's Pokemon Summer Camp (and seeing Serena blushing a lot when she's around Ash), the secret wasn't very hidden to me. Love found the future queen and she was wishing her lover to be her king. I just wished the king could have been my big brother.

***Crash!***

Suddenly, a loud crashing sound startled us, awaking Ash and Serena from their wishes. For a moment, we began wondering what the noise was, but then the answer was caught within my sight after I turned towards the tents. Or Ash's tent to be more precise.

"What was that?" Ash wondered.

"Uh, Serena?" I called the brunette, pointing to her tent.

"I think you tent ate your stuff." I teased.

As jokingly as it sounded, it was technically true. Serena's purple tent (which looked like a face) fell apart, keeping all of her belongings inside the wreckage. I couldn't tell what the tent was supposed to look like, but it was a cute looking tent. The top of the tent had a large yellow bow decorated with big googly eyes staring at us in front.

"Darn it!" Serena cursed, getting back on her feet.

"Do you need any help?" I offered my assistance.

"Sure." The brunette sighed.

"I think we should all help." Ash joined in.

"Chaaa…" Pikachu yawned.

And with that, the rest of the night had us getting ready for bed. Since tomorrow was going to be a big day for Ash and I, the best thing for all of us was a good night sleep before a gym battle. Unfortunately, my sleeping spot was blocked by the mouth of Serena's tent. If Serena and I were going to sleep together, we needed to keep her tent up through the night.

"You two push the outside and I'll help from inside." I exclaimed, crawling in the tent.

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**Please Review and Comment!**


	2. Chapter 2: Space Invaders

**Enjoy!**

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**The Skies of Lumiose City**

Unknown POV

"He's gone."

In an expected turn of events, I had lost my mechanical nemesis. Upon entering the planet's atmosphere, the Leader of the Space Pirates gained some more speed and flew out of my sight to an unknown part of the peaceful looking world. Our paths were now separate from each other, but I knew we were going to meet again.

Despite the mechanical dragon being a major threat to the world, destroying him wasn't my main objective. With the calm weather on my side, I descended my ship near a lid up city. In a quiet forest area that was east to the lively city and wasn't going to attract my presence to any human or Space Pirate. As my ship landed in a large open area of the forest, I prepared myself for my next mission. I equipped my suit with fourteen energy tanks to be my life support and 230 missiles loaded into my arm cannon.

I then went to the center of my tiny ship and activated the elevator, lowering me out to the wild. Out to the middle of the wilderness of this unknown planet. A wilderness that I didn't want to intrude with. As I began to depart from my ship, the first objective kept buzzing in my head. If I was going to prevent the Space Pirates from conquering this world, I needed to know more about the planet itself. I needed some information on the creatures of this world and the city seemed like a good place to start gaining some. From my ship, I took a left and then made my way towards the city lights.

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**Meanwhile in Prism Tower**

Normal POV

After a hard day of battling pokemon trainers, a peaceful night went underway for the Gym Leader's pokemon and his robotic substitute. An artificial robot named Clembot built to run and protect his creator's gym from intruders or thieves. Connected a bunch of wires for recharging, the gray colored robot was dreaming in his room, resting up for another big day of being the referee.

***BOOM!***

***BOOM!***

***BOOM!***

Unfortunately, the slumbering was interrupted by the sudden shakings of the tower. The robot became disconnected, knocking him down to the floor as he woke up to see the hard ground in front of him.

"Is it morning already?" The robot wondered.

The tower shook once more in response to the robot's question, convincing himself that the morning sun hasn't risen yet. As he struggled to keep himself steady, the substitute gym leader realized that something else was happening inside Prism Tower and it wasn't an earthquake in effect. He then rose back on his metallic feet and went to check on the pokemon.

"Luxray, is everything alright!?" Clembot called out while walking down the hall.

**"ROAR!"**

Clembot came to a complete halt to the sound of an unfamiliar roar, slowly turning to where he came from. Beyond the dark hallway, pair of yellow eyes beamed towards the frightened robot, heating up his circuits as the mysterious creature emerged from the shadows.

"Who are you?" The robot asked.

With a growl for an answer, the creature appeared in Clembot's eyes as he found out that it wasn't a pokemon. From where he stood, he watched a gray alien looking monster that had lobster-like claws, two-toed feet, a cannon on its right wrist, and a retractable scythe on the other wrist.

Before Clembot could react, the beast fired a shot of energy from its cannon. Clemont's robot quickly dodged the energy bullet in fear, breathing heavily at what was going on. The being before him didn't come to Prism Tower for a gym battle. It came for some destruction; which meant harming the pokemon as a bonus objective. Overwhelmed by the thought of death, Clembot had no choice but to do what he was built for. He turned his arms into arm cannons and gave his foe a dirty stare.

"The gym is closed!" Clembot announced.

Without another word, the co-gym leader frantically fired one of his arm cannons, blasting the monster into oblivion. It roared in great pain as its body was flung by the deadly shot before exploding without a single trace. No pieces of flesh or blood were left behind as Clembot realized that he had vaporized an alien. He then took a sighed in relief, knowing that he was still functional for another day.

**"ROAR!"**

Unfortunately, the night was still young as the robot heard the shrieks of more aliens approaching. He aimed his arm cannons towards the darkness and just as he expected, there were more of them. Three more aliens showed their exoskeletons in the dim light to avenge their fallen comrade, but they had another thing coming.

"Bring it on!" The robot ordered.

***BOOM!***

The tower shook once again, rattling everyone inside for a brief moment. As Clembot fought to stay still, the sounds of more aliens echoed from the darkness, alerting him that there were plenty of them left. He turned around and sure enough, four more came from the other side. With both ends blocked, Clemont's robot was surrounded by an unknown species of aliens.

"Where are they coming from?!" Clembot gasped.

Overwhelmed by the odds of survival, the co-gym leader quickly pointed stretched his arm cannons towards both ends of the hall and began eradicating the intruders. One by one he heard his victims explode as he gazed upon the door he came out from. The door to where he was recharging and where he could go to call for support.

"I need to warn the city about these ali…"

"GAHH!"

For a moment, Clembot felt the sudden urge of death as he suddenly lost his right arm. Like a Sceptile using Leaf Blade, he felt one of the beasts sliced his right arm cannon in an instant, leaving an opened shoulder sparking wildly and one arm cannon left working.

"MY ARM!" Clembot shrieked.

The creature responsible for the strike slid in front of the damaged robot and let out a roar of rage. A slimy mouth with sharp fangs was shown to the victim as a message to die, but it wasn't enough to stop him. Rage also flew the robot's circuits as he replied by another shot from his left arm cannon.

"Need to… get to… the alarm." The co-gym leader struggled to say, heading back to his room.

As he felt the energy leaking out of his system, the door opened up in Clembot's favor, allowing him to locate the emergency alarm switch. The search didn't last for a minutes since the switch was next to the doorway. A tiny red box stuck out from the brown colored wall and was accessible for anyone to use in case of an emergency. Fires were a common reason to pull the switch, but an alien invasion was the rarest excuse to set off an alarm. With little strength left, Clembot went to the switch, grabbed the handle with his only hand, and pulled it out from the box. The alarm began blaring loudly as Clembot's creation collapsed onto the golden floor, praying for help with his last breath.

"H-help us… Clemont."

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**Please Review and Comment!**

**Also, thanks for the feedback on the first chapter. I know it was hard to replaced the old version, but I think this version will be much better.**


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